When the announcement came through, John didn't have time to apply his 'make-up'; even after expecting the ship for a while, on another level it was hard to adjust to the idea that the SGC could spare more ships for Pegasus rather than them relying on Orion and the occasional visit from Daedalus.

It was a strange thing to find unnerving, but the last few weeks had been the quietest time he could ever remember since he'd arrived in Pegasus. He was aware that the Wraith were still out there in the wider galaxy, but all of their allies had reported that there was no sign of approaching hive-ships, and there had been little contact with the Wraith during their more standard trips through the Stargate. He was aware that things had been busy back in the Milky Way galaxy, following the mass suicide of the Asgard and the subsequent final defeat of the Ori armies, but aside from it meaning that Earth could spare more resources to help Atlantis, the final defeat of the Ori didn't really impact his regular routine that much.

At the moment, it was almost pleasant to only have to worry about a few personal issues rather than bigger threats. Carson had reported that his new deputy chief of medicine, a Doctor Jennifer Keller, was having some trouble with the pressure of her new role, but he and Elizabeth had each assured her that they were comfortable with her staying where she was despite that. McKay was having trouble with his yearly performance reviews, protesting that he didn't really know most of the people who worked in the city by name, but Elizabeth had countered that if John was making the effort he certainly should (Even if John didn't find himself with much more to say than to confirm the high standards of everyone in the military division of the city.

Still, going over all the personnel files to make sure that there was nobody he needed to single out for particular attention had taken time, with the result that John had been in his quarters when he'd received the message that the Apollo had arrived ahead of schedule. Quickly finishing his current sentence, John saved his work and hurried to the briefing room after putting on his mask; he didn't want to waste time applying his make-up for someone who should already know what he looked like. By the time he reached the conference room, Elizabeth and McKay were already sitting around the table with two folders in front of them, along with an unfamiliar man with dark skin and a completely bald head, looking at John with a slight smile as he entered.

"John Sheppard, I presume?"

"The mask gives it away, right?" John said, shaking the other man's hand as he took the offered folder. "Sorry about not being here; end-of-year evaluations, you know…"

"He does those?" McKay looked at Elizabeth indignantly. "He's only been in charge a few months; shouldn't someone else do that?"

"He's been in the city before we were, Doctor; I think we can assume that John knows what his staff are capable of," Elizabeth said, shooting an apologetic glance at John before she turned back to the other man. "Well, Colonel Ellis, now that John's here, what's this briefing you wanted to talk to us about?"

"Ever since the human-form Replicators made a play for the city, we've had the Daedalus make regular reconnaissance fly-bys of their home planet."

"Which we know," John noted as he sat down beside Elizabeth.

"Two months ago, it took these pictures," Ellis said, activating a projector to display a photograph of large, flat areas on what was some kind of planet surface.

"I'm sorry, what am I supposed to be looking at here?" Elizabeth asked, staring thoughtfully at the screen.

"Nothing."

"Eh?" John cut in, wondering if this was some kind of military psyche-out he hadn't learned about.

"This image," Ellis continued, the projector now showing the same area with arrows indicating objects that hadn't been there before, "was taken about three weeks ago in the very same location. They're building ships; a lot of them."

"And nobody told us about this earlier because…?" John asked, looking at Ellis with a pointed glare.

"We were making plans back on Earth," Ellis replied, countering John's glare with his own.

"Well, if they're coming for us, we should start making preparations to bolster the shield," McKay cut in. "I mean, we should-"

"They're not gonna get here," Ellis said firmly. "I'm here to inform you that in precisely twelve hours, the Apollo, in consort with your team, will launch a surgical strike on the Replicator planet."

"OK… When you say 'set', how many are we talking here?" John inquired.

"The Horizon carries six warheads and four decoys," Ellis said, before looking over at McKay. "I'm gonna need you to do a final inspection before we-"

"Hold on; six nukes against Replicators?" John cut in. "I grant that I've only met the local ones, but I read the files when I was on Earth; can you really blow them up when they've got that whole 'self-replicating' thing going on?"

"The Milky Way ones were self-replicating, yes, but these ones aren't," Ellis clarified. "Their ships aren't built from nano-cells; they're constructed of real material that can be destroyed. Six will be more than enough for now."

"Which one's that again?" Elizabeth asked before John had to ask it; this new job required him to keep so many acronyms straight it was easy to miss a few.

"Planetary Wide Anti-Replicator Weapons," McKay clarified before turning back to Ellis. "Look, the Asgard were capable of creating a satellite that could wipe out an entire Replicator planet. I mean, we've had some trouble making one of our own but-"

"Look, would I prefer taking out an entire planet at once?" Ellis began.

"OK, I think we should all be clear that it's the Replicators that are the problem; we're not here to blow up the damn planet just because we can-" John cut in.

"The point," Ellis continued with a pointed glare at John, "is that this image is giving the IOA a lot of sleepless nights. The Replicators know the location of Earth and, with these new ships, have the means to get there; we can't just sit on our hands while the guys at Area 51 try to come up with a solution."

"…OK, I get that," John said, shaking his head in resignation.

"This mission's primary objective is to eliminate key military targets; we'll come back and finish once the new weapon is up and running," Ellis said, turning back to McKay. "Doctor, I'm gonna need you to start your inspections as soon as possible."

McKay had barely begun to stammer out his acknowledgement before Ellis had given the order to beam the Canadian scientist to the ship, leaving Ellis to pick up the photographs and leave the briefing room as though the issue of what to do next was already decided.

"Can you believe this?" Elizabeth asked, standing up to look at the photo still on the screen.

"I know," John said, getting up to study the image beside Elizabeth. "I'm all for taking out the Replicators, but diving in like this before we're completely ready…"

"You don't agree?"

"I'm… not entirely comfortable with their decision," John said, shrugging awkwardly at the city's leader after a moment's thought. "I get where the IOA are coming from, and I think we can safely say that those ships make it clear the Asurans are after more than just Atlantis, but attacking when we can see that they're not ready to do anything and we've just got to wait a bit longer to get something that can put them all down at once…"

"You feel that we'd be knocking down a hornet's nest with a broom when we just need to wait a week for the pesticide?"

"…Longer time frame, but the analogy sounds about right," John acknowledged with a brief shrug. "Granted, I was never one for gardening or pest control…"

"I'll try and have another word with Colonel Ellis to discuss this," Elizabeth said, smiling gratefully at John; he might not be a trained soldier in the same way as other members of the expedition, but he was developing a keen insight into the enemy in Pegasus that she knew for a fact SG-1 in particular had come to respect during their crash course with him.

She didn't want to use him as a reference in case certain parties in the IOA decided that this meant that John was proving to be a difficult military commander, but the knowledge that he agreed with her doubts made her feel better.

When he checked in on Elizabeth in her office a couple of hours later, she looked so frustrated that John briefly thought about leaving her until she'd cooled down, but reminded himself of all the times she'd managed to get him to open up when he hadn't realised he needed to; if she could do it for him, he could do it for her.

"What's up?" he asked, looking curiously at her as he walked into the office.

"Just…" Elizabeth began, before sighing in frustration. "Have you ever had one of those days when you feel like you're just here because people needed someone to sign everything?"

"What?"

"I tried to tell Colonel Ellis that using nuclear weapons would be an ineffectual first strike, but as far as he was concerned, the IOA don't think that we can waste time with pointless negotiations and that's that. I mean, he actually told me that I don't have the authority to tell him to stand down and basically stated that my input doesn't matter-!"

"It does to me," John noted, cursing himself as soon as the words were past his lips.

"I mean…" he said, shrugging uncomfortably as Elizabeth looked at him, "I get that some people back on Earth think you might not be the best choice for this role now that they know there's a war here, but seriously, you think I didn't get a few critics when I was… well, 'applying' for this job? You're never going to please everybody, but that doesn't mean you should doubt yourself?"

"I spoke to General O'Neill and Mr Woolsey, but they both stand by the IOA's decision even when I'm the one out here assessing the situation directly; every time there's a major problem, it seems like the military just wants to step in and assuming control…"

"If that was the case, I think we can both agree I wouldn't be here."

"Pardon?"

"I said it when the siege began, and I'll say it again; you are the only leader of Atlantis I would ever obey without question," John said firmly. "If people back on Earth don't think you should be here, I doubt they'd have let you pull all the strings needed to let me take over the military contingent here, to say nothing of everything you must have gone through to make my role here official."

"Well… General O'Neill and Mr Woolsey helped-"

"After you made the original suggestion; they might have been overruled by the naysayers back on Earth this time around, but you can't start doubting yourself because some people think you aren't doing the job they'd want you to do," John said firmly. "You have the faith of the right people, and that's all that should matter to you."

"Thanks," Elizabeth said, smiling gratefully at him before her smile faltered. "For what it's worth, McKay's confirmed that the weapons platform is viable and ready to be deployed."

"Doesn't mean you're happy about it, right?"

"I understand that we could probably never negotiate with machines that have been nurturing their grudge against the Ancients and us for millennia, but that doesn't change the fact that I feel that deploying nukes instead of a specific anti-Replicator weapon is a mistake."

"How about McKay?" John asked. "If he says the platform isn't ready-?"

"He's already confirmed that it is," Elizabeth cut in. "Zelenka thought about trying to say the platform wasn't ready, or maybe even make sure of it, but McKay just didn't feel comfortable going that far even if he disagrees with the situation."

"Ah," John shrugged. "That must be why Ellis requested Lorne head up to the Apollo earlier."

"Lorne?" Elizabeth noted in surprise.

"Something about wanting a trained professional there to provide an experienced perspective on the whole thing," John said. "Personally, I think they just didn't want me up there because I made my stance clear."

"Your 'stance'?"

"If you don't like a plan, I don't like a plan; Colonel Ellis might not be able to kick me out of Atlantis, but he could make sure I wasn't in a position to show that," John clarified.

"Right," Elizabeth smiled, grateful for John's show of solidarity.

It might not change the minds of anyone back on Earth, but knowing that John Sheppard had that kind of faith in her leadership despite their contrasting styles and experiences…

Elizabeth couldn't place why that made her feel so much better, but it did.